/*
* Calign.c - compare two very similar sequences with restricted affine gap penalties.
*
* Written by Kun-Mao Chao (kmchao@csim.pu.edu.tw)
*/
/*
* Calign.driver.c - a sample program for calling sim4.
*
* Written by Kun-Mao Chao (kmchao@csim.pu.edu.tw)
*
* The command syntax is
* Calign file1 file2 [gap_limit [dist_limit]]
* where file1 and file2 contain arbitrary sequences of characters. It is
* assumed that the two character strings are very similar. Calign reports
* an alignment of the two sequences.
*
* The parameter gap_limit specifies that the insertion gaps
* of more than gap_limit symbols are
* penalized by gap_limit+1.
* The parameter dist_limit specifies the tolerable distance limit.
*
*/